dbgap_study_info.Rmd

---
title: "dbGaP study info"
output: html_document
date: "`r Sys.Date()`"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, results = 'asis')
source("fetch_dbgap_info.R")
```


```{r}
phs <- "phs000280"
version <- 8
study.xml <- fetch_study_xml(phs)
```

## Study version

```{r}
vers <- xml_version(study.xml, version)
cat(phs, "\n\n")
cat("version:", vers$version, "\n\n")
cat("participant set:", vers$participant_set, "\n\n")
```

## Consent and Data Use Limitations

Link to pheno variable summaries:

`r paste0("https://ftp.ncbi.nlm.nih.gov/dbgap/studies/", phs, "/", phs, ".v", vers$version, ".p", vers$participant_set, "/pheno_variable_summaries/")`

Click on link ending in "Subject.data_dict.xml" to view consent codes.

```{r}
cons <- xml_consent(study.xml, version)
for (i in 1:nrow(cons)) {
    cat("###", cons$consent_code[i], "\n\n")
    cat(cons$DUL[i], "\n\n")
}
```

## GSR posting

```{r}
cat(xml_gsr(study.xml, version))
```

## Acknowledgements

```{r}
cat(xml_acknowledgements(study.xml, version))
```